The film opens with the sentencing of Jean-Baptiste Grenouille, portrayed by Ben Whishaw, a notorious murderer. As the execution approaches, his life unfolds through a series of flashbacks, starting with his abandonment at birth amidst the chaotic aroma of a French fish market. Growing up in an orphanage, Grenouille becomes a peculiar boy, developing a superhuman sense of smell.
As he matures and works as a tanner's apprentice, he makes his first journey to Paris, where he becomes immersed in the myriad of new scents. During this time, he encounters a gentle girl selling plums, whose name is not explicitly mentioned, but her presence captivates him. In a tragic turn of events, he accidentally suffocates her in a moment of panic as he attempts to silence her shock at his behavior. Stripped of her clothes, Grenouille is left with the haunting memory of her scent, igniting an obsession to capture it forever.
After delivering goods to a perfume shop, Grenouille impresses the Italian perfumer Giuseppe Baldini (played by Dustin Hoffman) with his extraordinary talent for fragrance creation. This newfound partnership revitalizes Baldini's career, as Grenouille demands only one thing in return: to learn how to transform scents into exquisite perfumes. Baldini reveals that every perfume is a harmonious blend of twelve individual scents, with possibilities of a theoretical thirteenth essence. He recounts a mesmerizing tale of a perfume from an Egyptian tomb that once made everyone believe they were in paradise the moment it was uncorked.
Yet, when Grenouille realizes that Baldini's techniques cannot preserve every scent—particularly of inanimate objects or rotting corpses—he succumbs to despair. Inspired by a letter from Baldini, he sets out for Grasse in search of a different approach. During his journey, he grapples with the unsettling realization that he lacks a personal scent, feeling like a mere phantom. Driven by this revelation, he vows to create the perfect fragrance that would bestow him with identity and worth.
Upon reaching Grasse, Grenouille is captivated by the scent of the innocent Laura Richis (played by Rachel Hurd-Wood), the daughter of the affluent Antoine Richis (Alan Rickman). Determined to make her the "thirteenth scent" in his masterpiece, he secures employment under Madame Arnulfi (Corinna Harfouch) and Dominique Druot (Paul Berrondo), learning the art of enfleurage. However, his dark tendencies emerge as he murders a lavender picker, only to fail at preserving her scent through hot enfleurage. Undeterred, he then successfully captures the scent of a prostitute using cold enfleurage, setting off a string of murders targeting beautiful young women, all in pursuit of their fragrances.
As Grenouille disposes of the bodies around Grasse, fear sweeps through the town. After he successfully gathers a dozen scents, he prepares for his final act involving Laura. Amidst a church sermon condemning him, a local man falsely confesses to the murders, leaving Richis unconvinced as he tries to protect his daughter. Grenouille, however, tracks Laura down and sneaks into her room under the guise of night, ultimately taking her life.
Captured by soldiers post-murder, Grenouille prepares to meet his end, but not before applying his final creation of perfume. On the day of his execution, the scent he emits is so intoxicating that it captivates the crowd, leading them to deem him "innocent," resulting in a chaotic orgy. Even Richis, still convinced of Grenouille's guilt, is overtaken by the fragrance and embraces him.
When the town wakes up to the aftermath, they absolve Grenouille of the heinous crimes he committed, instead convicting Druot for the murders due to circumstantial evidence. Free from his execution, Grenouille possesses enough of his perfected perfume to have ultimate control over the world. Yet, he realizes that this power does not grant him the ability to love or be loved in return. Disillusioned, he returns to Paris, where his life began.
In a final act of defiance and the overwhelming need to connect, Grenouille returns to the very fish market of his birth and douses himself in his perfume. The ecstatic crowd gathers, believing him an angel, consuming him until nothing remains but his clothes and an open perfume bottle, from which a single droplet of his elusive scent dramatically falls.
